TB-Profiler result

Run: SRR1141261
Summary

Run ID: SRR1141261

Sample name:

Date: 02-04-2023 21:00:16

Number of reads: 82560

Percentage reads mapped: 1.18

Strain: lineage4.9

Drug-resistance: MDR-TB

Download CSV Download TXT Download PDF Download JSON
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations
Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family Main Spoligotype RDs Frequency
lineage4 Euro-American LAM;T;S;X;H None 0.97
lineage4.9 Euro-American (H37Rv-like) T1 None 0.97
Drug resistance-Associated Mutations: This table reports mutations found in candidate resistance genes which have been associated with drug resistance
Gene Chromosome position Mutation Type Estimated fraction Drugs
rpoB 761110 p.Asp435Val missense_variant 1.0 rifampicin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
ethA 4326333 p.Ala381Pro missense_variant 1.0 ethionamide
gid 4407967 p.Leu79Ser missense_variant 1.0 streptomycin
Non-Associated Mutations: This table reports mutations found in candidate resistance genes which have not been associated with drug resistance
Gene Chromosome position Mutation Type Estimated fraction
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 1.0
rpoB 762879 p.Met1025Leu missense_variant 1.0
rpoC 762894 c.-476C>T upstream_gene_variant 1.0
rpoC 762899 c.-471G>C upstream_gene_variant 1.0
rpoB 762911 p.Ile1035Met missense_variant 1.0
rpoC 762917 c.-453C>G upstream_gene_variant 1.0
rpoC 762920 c.-450C>T upstream_gene_variant 1.0
rpoC 762923 c.-447C>G upstream_gene_variant 1.0
rpoC 762929 c.-441G>T upstream_gene_variant 1.0
rpoB 762939 p.Met1045Leu missense_variant 1.0
rpoB 762942 p.Ile1046Val missense_variant 1.0
rpoC 762947 c.-423C>G upstream_gene_variant 1.0
rpoC 762971 c.-399G>C upstream_gene_variant 1.0
rpoC 762989 c.-381G>T upstream_gene_variant 0.93
rpoC 762995 c.-375G>T upstream_gene_variant 0.91
rpoC 762998 c.-372G>A upstream_gene_variant 0.89
rpoB 763123 p.Ile1106Thr missense_variant 1.0
rpoC 764332 c.963G>A synonymous_variant 0.67
rpoC 764353 c.984G>C synonymous_variant 0.67
rpoC 764365 c.996C>T synonymous_variant 0.67
rpoC 764371 c.1002G>T synonymous_variant 1.0
rpoC 764380 c.1011G>C synonymous_variant 0.67
rpoC 764387 c.1018T>C synonymous_variant 1.0
rpoC 764398 c.1029G>C synonymous_variant 0.67
rpoC 764404 c.1035C>T synonymous_variant 0.67
rpoC 764405 c.1036_1038delAGGinsCGC synonymous_variant 1.0
rpoC 764605 c.1236G>C synonymous_variant 0.67
rpoC 764611 c.1242G>T synonymous_variant 0.67
rpoC 764623 c.1254C>G synonymous_variant 0.79
rpoC 764632 c.1263T>C synonymous_variant 0.94
rpoC 764635 c.1266C>G synonymous_variant 0.86
rpoC 764650 c.1281G>T synonymous_variant 1.0
rpoC 764665 c.1296C>G synonymous_variant 0.88
rpoC 764672 p.Gln435Thr missense_variant 0.96
rpoC 764686 c.1317C>T synonymous_variant 0.82
rpoC 764695 c.1326T>C synonymous_variant 0.93
rpoC 764716 c.1347G>C synonymous_variant 0.95
rpoC 764719 c.1350G>A synonymous_variant 0.92
rpoC 764722 c.1353G>C synonymous_variant 0.92
rpoC 764731 c.1362G>C synonymous_variant 0.86
rpoC 764858 p.Leu497Met missense_variant 0.75
rpoC 764875 c.1506C>G synonymous_variant 1.0
rpoC 764878 c.1509C>G synonymous_variant 1.0
rpoC 764887 c.1518G>T synonymous_variant 1.0
rpoC 764888 c.1519_1521delTTGinsCTC synonymous_variant 1.0
rpoC 764902 c.1533C>G synonymous_variant 1.0
rpoC 764911 c.1542A>G synonymous_variant 1.0
rpoC 764912 p.Met515Val missense_variant 1.0
rpoC 764918 p.Val517Ile missense_variant 1.0
rpoC 764935 c.1566T>C synonymous_variant 0.93
rpoC 764948 c.1579T>C synonymous_variant 0.92
rpoC 764953 c.1584G>C synonymous_variant 0.92
rpoC 764956 c.1587T>C synonymous_variant 0.92
rpoC 764958 p.Glu530Ala missense_variant 0.92
rpoC 764968 c.1599T>C synonymous_variant 0.92
rpoC 764995 c.1626C>T synonymous_variant 0.67
rrs 1472150 n.305T>A non_coding_transcript_exon_variant 0.67
rrs 1472153 n.308G>A non_coding_transcript_exon_variant 0.67
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.97
rrs 1472210 n.365A>T non_coding_transcript_exon_variant 0.94
rrs 1472214 n.369C>G non_coding_transcript_exon_variant 0.94
rrs 1472223 n.378C>G non_coding_transcript_exon_variant 0.78
rrs 1472228 n.383G>C non_coding_transcript_exon_variant 0.76
rrs 1472235 n.390G>C non_coding_transcript_exon_variant 0.96
rrs 1472240 n.395G>A non_coding_transcript_exon_variant 0.96
rrs 1472242 n.397C>T non_coding_transcript_exon_variant 0.94
rrs 1472251 n.406G>C non_coding_transcript_exon_variant 0.75
rrs 1472251 n.406G>T non_coding_transcript_exon_variant 0.88
rrs 1472252 n.407G>A non_coding_transcript_exon_variant 0.24
rrs 1472253 n.408G>T non_coding_transcript_exon_variant 0.66
rrs 1472256 n.411T>A non_coding_transcript_exon_variant 0.64
rrs 1472259 n.414C>A non_coding_transcript_exon_variant 0.88
rrs 1472278 n.433C>T non_coding_transcript_exon_variant 0.4
rrs 1472344 n.499C>T non_coding_transcript_exon_variant 0.6
rrs 1472380 n.535G>C non_coding_transcript_exon_variant 0.75
rrs 1472382 n.537G>A non_coding_transcript_exon_variant 0.75
rrs 1472389 n.544G>A non_coding_transcript_exon_variant 0.67
rrs 1472390 n.545T>A non_coding_transcript_exon_variant 0.67
rrs 1472391 n.546C>T non_coding_transcript_exon_variant 0.67
rrs 1472707 n.862A>G non_coding_transcript_exon_variant 0.33
rrs 1472709 n.864T>G non_coding_transcript_exon_variant 0.33
rrs 1472714 n.869A>T non_coding_transcript_exon_variant 0.4
rrs 1472715 n.870C>G non_coding_transcript_exon_variant 0.4
rrs 1472716 n.871C>A non_coding_transcript_exon_variant 0.62
rrs 1472734 n.889C>T non_coding_transcript_exon_variant 0.82
rrs 1472741 n.896G>A non_coding_transcript_exon_variant 0.82
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.9
rrs 1472767 n.922G>A non_coding_transcript_exon_variant 0.9
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.92
rrs 1472785 n.940G>T non_coding_transcript_exon_variant 0.89
rrs 1472786 n.941C>G non_coding_transcript_exon_variant 0.89
rrs 1472814 n.969G>A non_coding_transcript_exon_variant 0.84
rrs 1473035 n.1190G>A non_coding_transcript_exon_variant 0.33
rrs 1473139 n.1294T>C non_coding_transcript_exon_variant 0.36
rrs 1473147 n.1302G>T non_coding_transcript_exon_variant 0.61
rrs 1473148 n.1303G>A non_coding_transcript_exon_variant 0.7
rrs 1473163 n.1318C>T non_coding_transcript_exon_variant 0.79
rrs 1473164 n.1319C>A non_coding_transcript_exon_variant 0.8
rrs 1473172 n.1327T>C non_coding_transcript_exon_variant 0.68
rrs 1473173 n.1328C>T non_coding_transcript_exon_variant 0.71
rrs 1473177 n.1332G>A non_coding_transcript_exon_variant 0.8
rrs 1473192 n.1347A>G non_coding_transcript_exon_variant 0.82
rrs 1473205 n.1360T>C non_coding_transcript_exon_variant 0.82
rrs 1473226 n.1381C>T non_coding_transcript_exon_variant 0.88
rrs 1473248 n.1403G>A non_coding_transcript_exon_variant 1.0
rrs 1473249 n.1404T>C non_coding_transcript_exon_variant 1.0
rrs 1473352 n.1507C>T non_coding_transcript_exon_variant 0.8
rrl 1475783 n.2126T>G non_coding_transcript_exon_variant 0.25
rrl 1475787 n.2130C>T non_coding_transcript_exon_variant 0.25
rrl 1475803 n.2146T>C non_coding_transcript_exon_variant 0.29
rrl 1475804 n.2147G>C non_coding_transcript_exon_variant 0.29
rrl 1475816 n.2159C>G non_coding_transcript_exon_variant 0.45
rrl 1475817 n.2160A>G non_coding_transcript_exon_variant 0.56
rrl 1476311 n.2654G>C non_coding_transcript_exon_variant 0.6
rrl 1476312 n.2655T>C non_coding_transcript_exon_variant 0.6
rrl 1476313 n.2656G>A non_coding_transcript_exon_variant 0.71
rrl 1476336 n.2679C>T non_coding_transcript_exon_variant 0.96
rrl 1476338 n.2681C>T non_coding_transcript_exon_variant 0.96
rrl 1476356 n.2699C>A non_coding_transcript_exon_variant 0.97
rrl 1476357 n.2700T>C non_coding_transcript_exon_variant 0.97
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.97
rrl 1476359 n.2702C>G non_coding_transcript_exon_variant 0.97
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.96
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.96
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.96
rrl 1476383 n.2726T>G non_coding_transcript_exon_variant 0.96
rrl 1476384 n.2727G>T non_coding_transcript_exon_variant 0.96
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.97
rrl 1476411 n.2754G>T non_coding_transcript_exon_variant 0.97
rrl 1476425 n.2768G>T non_coding_transcript_exon_variant 0.95
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.94
rrl 1476442 n.2785T>A non_coding_transcript_exon_variant 0.9
rrl 1476443 n.2786G>T non_coding_transcript_exon_variant 0.9
rrl 1476455 n.2798C>A non_coding_transcript_exon_variant 0.89
rrl 1476456 n.2799A>T non_coding_transcript_exon_variant 0.89
rrl 1476463 n.2806C>A non_coding_transcript_exon_variant 0.87
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.97
rrl 1476470 n.2813C>T non_coding_transcript_exon_variant 0.87
rrl 1476483 n.2826G>A non_coding_transcript_exon_variant 0.83
rrl 1476501 n.2844C>T non_coding_transcript_exon_variant 0.7
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.89
rpsA 1834177 c.636A>C synonymous_variant 0.8
PPE35 2167926 p.Leu896Ser missense_variant 1.0
Rv1979c 2221939 p.Arg409Gln missense_variant 1.0
thyA 3073953 c.519T>C synonymous_variant 1.0
thyA 3073956 c.516G>C synonymous_variant 1.0
thyA 3073959 c.513T>C synonymous_variant 1.0
thyA 3073962 p.Leu170Ile missense_variant 1.0
thyA 3073977 c.495A>G synonymous_variant 1.0
thyA 3073989 c.483T>C synonymous_variant 1.0
thyA 3073992 c.478_480delAGCinsTCG synonymous_variant 1.0
thyA 3073999 p.Arg158Lys missense_variant 1.0
thyA 3074004 c.468T>C synonymous_variant 1.0
thyA 3074010 c.462C>G synonymous_variant 1.0
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
clpC1 4039691 c.1014G>T synonymous_variant 0.67
clpC1 4039697 c.1008C>T synonymous_variant 0.67
clpC1 4039700 c.1005C>T synonymous_variant 0.67
clpC1 4039724 c.981A>G synonymous_variant 0.5
clpC1 4039727 c.978C>T synonymous_variant 0.5
clpC1 4039730 c.975C>G synonymous_variant 0.5
clpC1 4039739 c.966C>G synonymous_variant 0.5
embA 4243460 c.228C>T synonymous_variant 1.0